IIT Jodhpur
Rotational Diffusion of Proteins in Nanochannels

Domain: Physics: Soft Condensed Matter Physics
 
Abstract
The research focuses on studying the effects of confinement on the rotational diffusion of a protein to understand the mechanistic features of biomolecules in both crowded and confined environments. We conducted coarse-grained molecular dynamics simulations of ubiquitin in cylindrical nanopore environments with different size.  
Our simulation reveals a 2-fold reduction in magnitude from the bulk rotational diffusion coefficient value as the confinement radius reaches double the size of protein’s hydrodynamic radius. However, the changes in the rotational diffusion coefficient are relatively small compared to the changes in the translational diffusion coefficient. Interestingly, the rotational anisotropy also varies considerably when pore radii approach protein dimensions. Our simulations point out that the confinement effects cause the breakdown of small angular displacement theory when the pore radius is close to the protein hydrodynamic radius.  

Reference:

Navaneeth Haridasan, Sridhar Kumar Kannam, Santosh Mogurampelly and Sarith P Sathian

  1. Phys. Chem. B (2019), 12323, 4825-4832

https://doi.org/10.1021/acs.jpcb.9b00895